{bio}[foss/2023a] dorado v0.8.3 w/ CUDA 12.1.1 #21996

pavelToman · 2024-12-10T10:05:10Z

(created using eb --new-pr)
resolves vscentrum/vsc-software-stack#468

github-actions · 2024-12-10T10:05:39Z

Updated software `dorado-0.8.3-foss-2023a-CUDA-12.1.1.eb`

Diff against dorado-0.8.0-foss-2023a-CUDA-12.1.1.eb

easybuild/easyconfigs/d/dorado/dorado-0.8.0-foss-2023a-CUDA-12.1.1.eb

diff --git a/easybuild/easyconfigs/d/dorado/dorado-0.8.0-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/d/dorado/dorado-0.8.3-foss-2023a-CUDA-12.1.1.eb
index 778c00e0d6..8432e8fcef 100644
--- a/easybuild/easyconfigs/d/dorado/dorado-0.8.0-foss-2023a-CUDA-12.1.1.eb
+++ b/easybuild/easyconfigs/d/dorado/dorado-0.8.3-foss-2023a-CUDA-12.1.1.eb
@@ -1,7 +1,7 @@
 easyblock = 'CMakeMake'
 
 name = 'dorado'
-version = '0.8.0'
+version = '0.8.3'
 versionsuffix = '-CUDA-%(cudaver)s'
 
 homepage = 'https://github.com/nanoporetech/dorado'
@@ -21,9 +21,8 @@ sources = [{
     'filename': SOURCE_TAR_GZ,
 }]
 patches = [
-    '%(name)s-%(version)s_dont_install_external_libraries.patch',
+    '%(name)s-0.8.0_dont_install_external_libraries.patch',
 ]
-
 checksums = [
     None,
     '28942b7057af00c574a5e70d33a58b4036fd09ae0b041f45b67581c8dda832b1',

Diff against dorado-0.7.3-foss-2023a-CUDA-12.1.1.eb

easybuild/easyconfigs/d/dorado/dorado-0.7.3-foss-2023a-CUDA-12.1.1.eb

diff --git a/easybuild/easyconfigs/d/dorado/dorado-0.7.3-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/d/dorado/dorado-0.8.3-foss-2023a-CUDA-12.1.1.eb
index 9927f0492b..8432e8fcef 100644
--- a/easybuild/easyconfigs/d/dorado/dorado-0.7.3-foss-2023a-CUDA-12.1.1.eb
+++ b/easybuild/easyconfigs/d/dorado/dorado-0.8.3-foss-2023a-CUDA-12.1.1.eb
@@ -1,7 +1,7 @@
 easyblock = 'CMakeMake'
 
 name = 'dorado'
-version = '0.7.3'
+version = '0.8.3'
 versionsuffix = '-CUDA-%(cudaver)s'
 
 homepage = 'https://github.com/nanoporetech/dorado'
@@ -21,14 +21,11 @@ sources = [{
     'filename': SOURCE_TAR_GZ,
 }]
 patches = [
-    '%(name)s-%(version)s_include-fstream.patch',
-    '%(name)s-%(version)s_dont_install_external_libraries.patch',
+    '%(name)s-0.8.0_dont_install_external_libraries.patch',
 ]
-
 checksums = [
     None,
-    'a32cbd34185bcc5ae3d552a072e396825aa7184187cd11c70a4380618387a530',
-    '2a250d606c0ae17f47d99981309fa204a1394ddd81851a1d530dcd0aea2306ac',
+    '28942b7057af00c574a5e70d33a58b4036fd09ae0b041f45b67581c8dda832b1',
 ]
 
 builddependencies = [
@@ -63,6 +60,7 @@ preconfigopts += "sed -i '/Htslib.cmake/d' ../dorado/CMakeLists.txt && "
 # link with -lhts, not -lhtslib
 preconfigopts += "sed -i 's/htslib/hts/g' ../dorado/CMakeLists.txt && "
 preconfigopts += "sed -i 's/htslib/hts/g' ../dorado/dorado/utils/CMakeLists.txt && "
+preconfigopts += "sed -i 's/htslib/hts/g' ../dorado/dorado/torch_utils/CMakeLists.txt && "
 
 # disable treating warnings like errors by stripping out -Werror
 # cfr. https://github.com/nanoporetech/dorado/issues/779

Diff against dorado-0.6.1-foss-2023a-CUDA-12.1.1.eb

easybuild/easyconfigs/d/dorado/dorado-0.6.1-foss-2023a-CUDA-12.1.1.eb

diff --git a/easybuild/easyconfigs/d/dorado/dorado-0.6.1-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/d/dorado/dorado-0.8.3-foss-2023a-CUDA-12.1.1.eb
index 378a9deec6..8432e8fcef 100644
--- a/easybuild/easyconfigs/d/dorado/dorado-0.6.1-foss-2023a-CUDA-12.1.1.eb
+++ b/easybuild/easyconfigs/d/dorado/dorado-0.8.3-foss-2023a-CUDA-12.1.1.eb
@@ -1,7 +1,7 @@
 easyblock = 'CMakeMake'
 
 name = 'dorado'
-version = '0.6.1'
+version = '0.8.3'
 versionsuffix = '-CUDA-%(cudaver)s'
 
 homepage = 'https://github.com/nanoporetech/dorado'
@@ -20,10 +20,12 @@ sources = [{
     },
     'filename': SOURCE_TAR_GZ,
 }]
-patches = ['dorado-0.6.1_include-fstream.patch']
+patches = [
+    '%(name)s-0.8.0_dont_install_external_libraries.patch',
+]
 checksums = [
     None,
-    'a7692a2d67422d808b3b81f3a297b7b89299ab0091e5d01f0b8a9aee9b942377',
+    '28942b7057af00c574a5e70d33a58b4036fd09ae0b041f45b67581c8dda832b1',
 ]
 
 builddependencies = [
@@ -46,7 +48,6 @@ dependencies = [
 # don't link to OpenSSL static libraries
 # fix for CMake Error "missing: OPENSSL_CRYPTO_LIBRARY" (if only shared OpenSSL libraries are available)
 preconfigopts = "sed -i '/OPENSSL_USE_STATIC_LIBS TRUE/d' ../dorado/cmake/OpenSSL.cmake && "
-preconfigopts += "export OPENSSL_ROOT_DIR=$EBROOTOPENSSL && "
 # link in the ssl and crypto libs, to fix:
 # undefined reference to symbol 'SSL_get_peer_certificate@@OPENSSL_1_1_0'
 preconfigopts += "sed -i 's/OpenSSL::SSL/ssl\\n    crypto/g' ../dorado/dorado/utils/CMakeLists.txt && "
@@ -59,17 +60,23 @@ preconfigopts += "sed -i '/Htslib.cmake/d' ../dorado/CMakeLists.txt && "
 # link with -lhts, not -lhtslib
 preconfigopts += "sed -i 's/htslib/hts/g' ../dorado/CMakeLists.txt && "
 preconfigopts += "sed -i 's/htslib/hts/g' ../dorado/dorado/utils/CMakeLists.txt && "
+preconfigopts += "sed -i 's/htslib/hts/g' ../dorado/dorado/torch_utils/CMakeLists.txt && "
 
 # disable treating warnings like errors by stripping out -Werror
 # cfr. https://github.com/nanoporetech/dorado/issues/779
 preconfigopts += "sed -i 's/-Werror//g' ../dorado/cmake/Warnings.cmake && "
 
-configopts = "-DDORADO_INSTALL_PATH=%(installdir)s "
-configopts += "-DCUDA_TOOLKIT_ROOT_DIR=$EBROOTCUDA -DCMAKE_CUDA_COMPILER=$EBROOTCUDA/bin/nvcc "
-configopts += "-DDORADO_LIBTORCH_DIR=$EBROOTPYTORCH/lib "
-# add -pthread flag (in addition to -lpthread) to avoid linking error:
-# in function `_GLOBAL__sub_I_mutex.cc': mutex.cc:(.text.startup+0x17): undefined reference to `pthread_atfork'
-configopts += '-DCMAKE_C_FLAGS="$CFLAGS -pthread" '
+_copts = [
+    "-DCUDA_TOOLKIT_ROOT_DIR=$EBROOTCUDA",
+    "-DCMAKE_CUDA_COMPILER=$EBROOTCUDA/bin/nvcc",
+    '-DOPENSSL_ROOT_DIR=$EBROOTOPENSSL',
+    "-DDORADO_LIBTORCH_DIR=$EBROOTPYTORCH/lib",
+    # add -pthread flag (in addition to -lpthread) to avoid linking error:
+    # in function `_GLOBAL__sub_I_mutex.cc': mutex.cc:(.text.startup+0x17): undefined reference to `pthread_atfork'
+    '-DCMAKE_C_FLAGS="$CFLAGS -pthread"',
+]
+
+configopts = ' '.join(_copts) + ' '
 
 # disable CMake fiddling with RPATH when EasyBuild is configured to use RPATH linking
 configopts += "$(if %(rpath_enabled)s; then "

pavelToman · 2024-12-10T10:06:13Z

@boegelbot please test @ generoso

boegelbot · 2024-12-10T10:10:09Z

@pavelToman: Request for testing this PR well received on login1

PR test command 'EB_PR=21996 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs /opt/software/slurm/bin/sbatch --job-name test_PR_21996 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 14845

Test results coming soon (I hope)...

- notification for comment with ID 2531084812 processed

Message to humans: this is just bookkeeping information for me,
it is of no use to you (unless you think I have a bug, which I don't).

pavelToman · 2024-12-10T10:13:15Z

Test report by @pavelToman
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
node4012.donphan.os - Linux RHEL 8.8, x86_64, Intel(R) Xeon(R) Gold 6240 CPU @ 2.60GHz, 1 x NVIDIA NVIDIA A2, 545.23.08, Python 3.6.8
See https://gist.github.com/pavelToman/c059a3c50a13573f36e3f46ff123fe63 for a full test report.

boegelbot · 2024-12-10T10:24:27Z

Test report by @boegelbot
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
cns1 - Linux Rocky Linux 8.9, x86_64, Intel(R) Xeon(R) CPU E5-2667 v3 @ 3.20GHz (haswell), Python 3.6.8
See https://gist.github.com/boegelbot/bd09fc6118a2597da2dad517c3049fcb for a full test report.

pavelToman · 2024-12-10T10:29:58Z

@boegelbot please test @ jsc-zen3

boegelbot · 2024-12-10T10:30:19Z

@pavelToman: Request for testing this PR well received on jsczen3l1.int.jsc-zen3.fz-juelich.de

PR test command 'if [[ develop != 'develop' ]]; then EB_BRANCH=develop ./easybuild_develop.sh 2> /dev/null 1>&2; EB_PREFIX=/home/boegelbot/easybuild/develop source init_env_easybuild_develop.sh; fi; EB_PR=21996 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_21996 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 5423

Test results coming soon (I hope)...

- notification for comment with ID 2531148294 processed

Message to humans: this is just bookkeeping information for me,
it is of no use to you (unless you think I have a bug, which I don't).

boegelbot · 2024-12-10T10:38:13Z

Test report by @boegelbot
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
jsczen3c1.int.jsc-zen3.fz-juelich.de - Linux Rocky Linux 9.5, x86_64, AMD EPYC-Milan Processor (zen3), Python 3.9.19
See https://gist.github.com/boegelbot/db27f14f964e13da2cd4ee300834a0f5 for a full test report.

pavelToman · 2024-12-10T10:51:59Z

@boegelbot please test @ jsc-zen3-a100

boegelbot · 2024-12-10T11:00:14Z

@pavelToman: Request for testing this PR well received on jsczen3l1.int.jsc-zen3.fz-juelich.de

PR test command 'if [[ develop != 'develop' ]]; then EB_BRANCH=develop ./easybuild_develop.sh 2> /dev/null 1>&2; EB_PREFIX=/home/boegelbot/easybuild/develop source init_env_easybuild_develop.sh; fi; EB_PR=21996 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_21996 --ntasks=8 --partition=jsczen3g --gres=gpu:1 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 5424

Test results coming soon (I hope)...

- notification for comment with ID 2531220588 processed

Message to humans: this is just bookkeeping information for me,
it is of no use to you (unless you think I have a bug, which I don't).

boegelbot · 2024-12-10T11:06:05Z

Test report by @boegelbot
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
jsczen3g1.int.jsc-zen3.fz-juelich.de - Linux Rocky Linux 9.5, x86_64, AMD EPYC-Milan Processor (zen3), 1 x NVIDIA NVIDIA A100 80GB PCIe, 555.42.06, Python 3.9.19
See https://gist.github.com/boegelbot/44bd716a2b005ef381cc0813d808800a for a full test report.

boegel

lgtm

boegel · 2024-12-11T13:28:11Z

Test report by @boegel
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
node3306.joltik.os - Linux RHEL 9.4, x86_64, Intel(R) Xeon(R) Gold 6242 CPU @ 2.80GHz (cascadelake), 1 x NVIDIA Tesla V100-SXM2-32GB, 555.42.06, Python 3.9.18
See https://gist.github.com/boegel/7aae4dce1bb4525f3c1e22bc007c61bb for a full test report.

boegel · 2024-12-11T16:23:14Z

Going in, thanks @pavelToman!

adding easyconfigs: dorado-0.8.3-foss-2023a-CUDA-12.1.1.eb

55fb0ee

pavelToman added the update label Dec 10, 2024

pavelToman mentioned this pull request Dec 10, 2024

dorado vscentrum/vsc-software-stack#468

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boegel added this to the release after 4.9.4 milestone Dec 11, 2024

boegel approved these changes Dec 11, 2024

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boegel merged commit a27088b into easybuilders:develop Dec 11, 2024
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{bio}[foss/2023a] dorado v0.8.3 w/ CUDA 12.1.1 #21996

{bio}[foss/2023a] dorado v0.8.3 w/ CUDA 12.1.1 #21996

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{bio}[foss/2023a] dorado v0.8.3 w/ CUDA 12.1.1 #21996

{bio}[foss/2023a] dorado v0.8.3 w/ CUDA 12.1.1 #21996

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Updated software dorado-0.8.3-foss-2023a-CUDA-12.1.1.eb

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Updated software `dorado-0.8.3-foss-2023a-CUDA-12.1.1.eb`